FAIRMol

TC359

Pose ID 14448 Compound 44 Pose 210

DB SELECTIONDocking pose analysis is being read from this database.
Compound detail Protein structures Back to compounds
Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
T22
L. donovani rab5a L. donovani
Ligand TC359

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
36.7 kcal/mol
Protein clashes
0
Internal clashes
11
Native overlap
contact recall 0.86, Jaccard 0.69, H-bond role recall 0.27
Burial
86%
Hydrophobic fit
88%
Reason: 11 internal clashes
11 intramolecular clashes 71% of hydrophobic surface is solvent-exposed (17/24 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.962 kcal/mol/HA) ✓ Good fit quality (FQ -9.28) ✓ Strong H-bond network (8 bonds) ✓ Deep burial (86% SASA buried) ✓ Lipophilic contacts well-matched (88%) ✗ Very high strain energy (36.7 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)
Score
-28.849
kcal/mol
LE
-0.962
kcal/mol/HA
Fit Quality
-9.28
FQ (Leeson)
HAC
30
heavy atoms
MW
402
Da
LogP
3.56
cLogP
Strain ΔE
36.7 kcal/mol
SASA buried
86%
Lipo contact
88% BSA apolar/total
SASA unbound
723 Ų
Apolar buried
546 Ų

Interaction summary

HB 8 HY 5 PI 1 CLASH 0 ⚠ Exposure 70%
🚨Solvent-exposed hydrophobic surface — desolvation penalty likely
71% of hydrophobic surface is solvent-exposed (17/24 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 24 Buried (contacted) 7 Exposed 17 LogP 3.56 H-bonds 8
Exposed fragments: phenyl (2/5 atoms exposed)phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (3 atoms exposed)
Final rank3.165Score-28.849
Inter norm-1.271Intra norm0.310
Top1000noExcludedno
Contacts23H-bonds8
Artifact reasongeometry warning; 11 clashes; 2 protein clashes; high strain Δ 36.4
Residues
ALA158 ALA24 ASN126 ASN41 ASP129 ASP68 GLN42 GLU43 GLU73 GLY23 GLY25 GLY71 LEU130 LYS127 LYS159 LYS26 PHE38 SER157 SER22 SER27 SER28 THR44 THR69

Protein summary

165 residues
Protein targetT22Atoms2561
Residues165Chains1
Residue summaryLEU:363; LYS:242; ALA:231; ARG:214; ILE:190; GLU:180; VAL:144; SER:143; PHE:140; ASN:112; THR:112; TYR:105; GLN:102; ASP:96; GLY:77; TRP:48

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
NameRAB5AContacts21
PoseOpen native poseHB0
IFP residues
ALA158 ALA24 ALA40 ASN126 ASN41 ASP129 GLN42 GLU21 GLU73 GLY23 GLY25 LEU130 LEU39 LYS127 LYS159 LYS26 PHE38 SER157 SER22 SER27 SER28
Current overlap18Native recall0.86
Jaccard0.69RMSD-
HB strict4Strict recall0.27
HB same residue+role3HB role recall0.27
HB same residue3HB residue recall0.27

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes
No clash · clashes detected for this pose.

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
230 0.5079880905865612 -1.05823 -27.4761 7 16 0 0.00 0.00 - no Open
299 0.6541166288479228 -0.854458 -23.1766 4 15 0 0.00 0.00 - no Open
235 0.9617741215431999 -1.12463 -25.229 6 14 0 0.00 0.00 - no Open
231 2.18855395233315 -0.988386 -20.5952 6 18 0 0.00 0.00 - no Open
229 2.2323899897137838 -1.22394 -27.7163 4 18 0 0.00 0.00 - no Open
218 2.2689055911488274 -0.78972 -23.284 2 18 1 0.05 0.00 - no Open
259 2.2729413366463573 -1.11623 -28.5408 6 22 0 0.00 0.00 - no Open
272 2.457874472716344 -0.902589 -22.2336 4 14 0 0.00 0.00 - no Open
177 2.6921673697430357 -0.935706 -23.0441 7 17 0 0.00 0.00 - no Open
260 3.0169256640293716 -1.16386 -28.6068 6 23 0 0.00 0.00 - no Open
210 3.164995907995662 -1.27123 -28.8488 8 23 18 0.86 0.27 - no Current
276 3.36488331222722 -0.679093 -13.4836 5 10 0 0.00 0.00 - no Open
250 3.403056279509119 -0.752278 -20.1012 5 15 0 0.00 0.00 - no Open
277 3.748241609510073 -0.734284 -18.7968 5 12 0 0.00 0.00 - no Open
363 4.041594586258085 -0.824173 -18.2023 6 18 0 0.00 0.00 - no Open
209 4.429054136335406 -1.09718 -26.8529 8 22 17 0.81 0.27 - no Open

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -28.849kcal/mol
Ligand efficiency (LE) -0.9616kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.276
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 30HA

Physicochemical properties
Molecular weight 402.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.56
Lipinski: ≤ 5
Rotatable bonds 10

Conformational strain (MMFF94s)
Strain energy (ΔE) 36.69kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 95.31kcal/mol
Minimised FF energy 58.63kcal/mol

SASA & burial

✓ computed
SASA (unbound) 722.7Ų
Total solvent-accessible surface area of free ligand
BSA total 622.1Ų
Buried surface area upon binding
BSA apolar 545.8Ų
Hydrophobic contacts buried
BSA polar 76.3Ų
Polar contacts buried
Fraction buried 86.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 87.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1488.8Ų
SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.
Receptor non-polar SASA 1368.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 525.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)